Contacts of the helix formed by residues 159 - 175 (chain D) in PDB entry 2NPP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLU* 3.0 20.8 + - - -
158D VAL* 1.3 78.4 - - - +
160D SER* 1.3 54.1 + - - +
161D ALA* 3.5 8.7 + - - +
162D VAL* 3.1 29.3 + - - +
163D LYS* 2.8 37.9 + - - +
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D VAL 4.0 0.4 + - - -
159D SER* 1.3 72.6 - - - +
161D ALA* 1.3 64.1 - - - +
162D VAL 3.1 0.3 + - - -
163D LYS* 3.2 13.0 + - - +
164D ALA* 2.9 23.4 + - - +
167D ARG* 5.0 1.4 + - - -
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D SER* 3.3 7.7 + - - +
160D SER* 1.3 78.5 - - - +
162D VAL* 1.3 59.3 + - + +
164D ALA* 3.2 14.9 - - - +
165D GLU* 3.1 25.3 - - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLU* 4.0 22.0 - - + +
129D VAL* 4.2 21.3 - - + -
133D LYS* 5.0 1.1 - - - +
158D VAL* 3.7 21.1 - - + -
159D SER* 3.1 21.3 + - - +
161D ALA* 1.3 76.4 - - + +
163D LYS* 1.3 68.3 - - - +
164D ALA 2.9 1.3 - - - -
165D GLU* 2.8 19.8 + - - +
166D LEU* 2.7 33.5 + - + +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TYR* 3.2 69.8 - - + +
156D PRO* 4.0 15.3 + - - +
158D VAL* 3.5 17.9 - - + -
159D SER 2.8 22.0 + - - +
160D SER* 3.5 11.9 - - - +
162D VAL* 1.3 71.8 - - - +
164D ALA* 1.3 64.9 + - - +
166D LEU* 2.9 4.0 + - - +
167D ARG* 2.8 29.9 + - - +
195D VAL 5.6 1.0 + - - -
197D GLU* 3.9 16.5 + - - +
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D SER 2.9 13.2 + - - +
161D ALA* 3.2 15.9 - - - +
163D LYS* 1.3 77.5 - - - +
165D GLU* 1.3 66.7 + - + +
167D ARG* 3.2 34.3 + - - +
168D GLN* 3.3 10.4 + - - +
171D ARG* 5.2 0.7 + - - -
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LYS* 3.4 33.1 + - - +
161D ALA* 3.1 13.9 - - - +
162D VAL* 2.8 38.1 + - - +
164D ALA* 1.3 73.6 - - + +
166D LEU* 1.3 66.5 + - - +
168D GLN* 2.9 17.9 + - - +
169D TYR* 3.1 21.7 + - + -
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 4.0 24.9 - - + -
132D VAL* 4.9 8.5 - - + -
133D LYS* 4.7 8.5 - - + -
151D PHE* 3.6 28.0 - - + -
154D CYS* 4.3 14.6 - - - -
155D TYR* 3.5 44.6 - - + -
158D VAL* 4.2 4.3 - - + -
162D VAL* 2.7 33.6 + - + +
163D LYS 2.9 6.4 + - - +
165D GLU* 1.3 72.2 - - - +
167D ARG* 1.3 63.3 + - - +
169D TYR* 2.9 18.8 + - + +
170D PHE* 2.9 12.7 + - - +
192D PHE* 5.1 0.7 - - + -
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Residues in contact with ARG 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TYR* 2.8 36.6 + - + +
160D SER 5.0 1.0 + - - -
163D LYS* 2.8 14.9 + - - +
164D ALA* 3.4 43.1 + - - +
166D LEU* 1.3 72.6 - - - +
168D GLN* 1.3 63.1 + - - +
170D PHE* 3.5 2.6 + - - +
171D ARG* 3.1 35.7 + - - +
192D PHE* 4.4 11.9 - - + -
196D LEU* 3.8 21.8 - - + -
197D GLU* 4.3 2.2 + - - -
200D ASN* 3.1 38.9 + - - +
204D GLU* 4.4 16.6 - - + +
208D MET* 4.8 3.8 - - + +
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Residues in contact with GLN 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA 3.3 6.7 + - - +
165D GLU* 2.9 14.2 + - - +
167D ARG* 1.3 77.8 - - - +
169D TYR* 1.3 67.9 + - + +
171D ARG* 2.7 56.9 + - - +
172D ASN* 2.9 42.2 + - - +
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Residues in contact with TYR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LYS* 3.6 63.1 - - + +
136D ALA* 3.8 21.0 - - + +
137D GLY* 4.9 5.8 - - - -
151D PHE* 3.9 16.4 - - + -
165D GLU* 3.1 27.8 + - + -
166D LEU* 2.9 9.3 + - - +
168D GLN* 1.3 81.7 - - + +
170D PHE* 1.3 63.4 - - - +
172D ASN* 2.9 26.0 + - + +
173D LEU* 3.0 15.3 + - - +
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D CYS* 4.4 11.7 - - + -
151D PHE* 3.7 38.7 - + + -
166D LEU 2.9 10.2 + - - +
167D ARG 3.8 4.9 - - - +
169D TYR* 1.3 76.8 - - - +
171D ARG* 1.3 63.3 + - - +
173D LEU* 3.1 16.9 + - + +
174D CYS* 3.1 24.0 + - - -
185D ALA* 3.6 28.7 - - - -
188D LYS* 4.1 7.2 - - + -
189D LEU* 3.7 34.1 - - + -
192D PHE* 3.1 46.7 - + + -
208D MET* 3.7 11.2 - - - -
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Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA 5.2 0.4 + - - -
167D ARG* 3.1 15.4 + - - +
168D GLN* 2.7 70.7 + - - +
170D PHE* 1.3 77.6 - - - +
172D ASN* 1.3 63.3 + - - +
174D CYS* 3.0 15.1 + - - +
175D SER* 3.2 13.0 + - - -
204D GLU* 3.6 36.7 + - - +
207D PRO* 6.2 3.4 - - - -
208D MET* 3.6 36.1 - - + -
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Residues in contact with ASN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D GLN* 2.9 45.3 + - - +
169D TYR* 3.3 18.7 - - + +
171D ARG* 1.3 75.8 - - - +
173D LEU* 1.3 61.0 + - + +
175D SER* 3.4 18.0 + - - +
176D ASP* 3.4 13.0 + - - +
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA* 4.2 15.9 - - + +
144D ARG* 3.9 40.8 - - + +
148D CYS* 3.8 17.5 - - - +
151D PHE* 3.3 40.2 - - + -
169D TYR 3.0 12.6 + - - +
170D PHE* 3.4 11.7 - - + +
171D ARG 3.1 0.4 - - - -
172D ASN* 1.3 74.5 - - + +
174D CYS* 1.3 66.0 + - - +
175D SER 3.1 0.2 - - - -
176D ASP* 3.1 22.9 + - - +
181D VAL* 3.7 15.8 - - + +
182D ARG* 4.4 1.6 - - - +
185D ALA* 3.9 14.0 - - + +
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Residues in contact with CYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D PHE* 3.1 32.8 + - - -
171D ARG 3.0 8.4 + - - +
173D LEU* 1.3 78.6 - - - +
175D SER* 1.3 57.6 + - - +
182D ARG* 3.3 21.7 - - - +
185D ALA* 3.7 16.2 - - - -
189D LEU* 4.7 0.9 - - - -
208D MET* 3.7 29.2 - - + -
211D ASN* 6.5 0.7 - - + -
212D LEU* 3.6 38.3 - - + +
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Residues in contact with SER 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D ARG 3.3 13.0 + - - -
172D ASN* 3.4 14.9 + - - +
173D LEU 3.1 0.4 - - - -
174D CYS* 1.3 78.2 - - - +
176D ASP* 1.3 63.7 + - - +
177D ASP* 3.8 3.8 + - - +
182D ARG* 4.5 2.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il